Additive Method for the Prediction of Protein−Peptide Binding Affinity. Application to the MHC Class I Molecule HLA-A*0201

2002 ◽  
Vol 1 (3) ◽  
pp. 263-272 ◽  
Author(s):  
Irini A. Doytchinova ◽  
Martin J. Blythe ◽  
Darren R. Flower
Keyword(s):  
Binding Affinity ◽  
Mhc Class I ◽  
Peptide Binding ◽  
Class I ◽  
Additive Method ◽  
Mhc Class I Molecule ◽  
Peptide Binding Affinity

QSAR method for prediction of protein-peptide binding affinity: Application to MHC class I molecule HLA-A*0201

2007 ◽  
Vol 26 (1) ◽  
pp. 246-254 ◽  
Author(s):  
Chunyan Zhao ◽  
Haixia Zhang ◽  
Feng Luan ◽  
Ruisheng Zhang ◽  
Mancang Liu ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Mhc Class I ◽  
Peptide Binding ◽  
Class I ◽  
Mhc Class I Molecule ◽  
Peptide Binding Affinity

scholarly journals NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

2017 ◽  
Vol 199 (9) ◽  
pp. 3360-3368 ◽  
Author(s):  
Vanessa Jurtz ◽  
Sinu Paul ◽  
Massimo Andreatta ◽  
Paolo Marcatili ◽  
Bjoern Peters ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Mhc Class I ◽  
Peptide Binding ◽  
Class I ◽  
Peptide Binding Affinity

scholarly journals A Specialist Macaque MHC Class I Molecule with HLA-B*27–like Peptide-Binding Characteristics

2017 ◽  
Vol 199 (10) ◽  
pp. 3679-3690 ◽  
Author(s):  
Natasja G. de Groot ◽  
Corrine M. C. Heijmans ◽  
Arnoud H. de Ru ◽  
George M. C. Janssen ◽  
Jan W. Drijfhout ◽  
...  
Keyword(s):  
Mhc Class I ◽  
Peptide Binding ◽  
Class I ◽  
Binding Characteristics ◽  
Mhc Class I Molecule

scholarly journals Structure and Peptidome of the Bat MHC Class I Molecule Reveal a Novel Mechanism Leading to High-Affinity Peptide Binding

2019 ◽  
Vol 202 (12) ◽  
pp. 3493-3506 ◽  
Author(s):  
Zehui Qu ◽  
Zibin Li ◽  
Lizhen Ma ◽  
Xiaohui Wei ◽  
Lijie Zhang ◽  
...  
Keyword(s):  
Mhc Class I ◽  
Peptide Binding ◽  
Class I ◽  
High Affinity ◽  
Mhc Class I Molecule ◽  
Affinity Peptide

scholarly journals Mapping the peptide binding groove of MHC class I

2021 ◽  
Author(s):  
Janine-Denise Kopicki ◽  
Ankur Saikia ◽  
Stephan Niebling ◽  
Christian G&uumlnther ◽  
Maria M. Garcia-Alai ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Mhc Class I ◽  
Peptide Binding ◽  
Essential Element ◽  
Native Mass Spectrometry ◽  
Class I ◽  
Peptide Antigens ◽  
Novel Approach ◽  
Peptide Binding Groove ◽  
Binding Groove

An essential element of adaptive immunity is the selective binding of peptide antigens by major histocompatibility complex (MHC) class I proteins and their presentation to cytotoxic T lymphocytes on the cell surface. Using native mass spectrometry, we here analyze the binding of peptides to an empty disulfide-stabilized HLA-A*02:01 molecule. This novel approach allows us to examine the binding properties of diverse peptides. The unique stability of our MHC class I even enables us to determine the binding affinity of complexes, which are suboptimally loaded with truncated or charge-reduced peptides. Notably, a unique erucamide adduct decouples affinity analysis from peptide identity alleviating issues usually attributed to clustering. We discovered that two anchor positions at the binding surface between MHC and peptide can be stabilized independently and further analyze the contribution of other peptidic amino acids on the binding. We propose this as an alternative, likely universally applicable method to artificial prediction tools to estimate the binding strength of peptides to MHC class I complexes quickly and efficiently. This newly described MHC class I-peptide binding affinity quantitation represents a much needed orthogonal, confirmatory approach to existing computational affinity predictions and has the potential to eliminate binding affinity biases and thus accelerate drug discovery in infectious diseases autoimmunity, vaccine design, and cancer immunotherapy.

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